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NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL1674 [new locus tag: SACOL_RS08540 ]
  • pan locus tag?: SAUPAN004217000
  • symbol: SACOL1674
  • pan gene symbol?: recD2
  • synonym:
  • product: recombinase D

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL1674 [new locus tag: SACOL_RS08540 ]
  • symbol: SACOL1674
  • product: recombinase D
  • replicon: chromosome
  • strand: -
  • coordinates: 1702192..1704669
  • length: 2478
  • essential: unknown other strains

⊟Accession numbers[edit | edit source]

⊟Phenotype[edit | edit source]

Share your knowledge and add information here. [edit]

⊟DNA sequence[edit | edit source]

  • 1
    61
    121
    181
    241
    301
    361
    421
    481
    541
    601
    661
    721
    781
    841
    901
    961
    1021
    1081
    1141
    1201
    1261
    1321
    1381
    1441
    1501
    1561
    1621
    1681
    1741
    1801
    1861
    1921
    1981
    2041
    2101
    2161
    2221
    2281
    2341
    2401
    2461
    ATGTCAGACCCTACACTATTTGATTATTCAATGATCAAAGGTACTGTTGAAGCGATATTG
    TTTCAAAACAGTGATAATTTTTATACAGTGCTTAAAGTAGATACTATTGAAACAAATGAA
    GACTTTGATACAATGCCAACTGTTGTAGGGTTTCTTCCGAATATTGTTGAAGGCGATGTC
    TACACATTTAAAGGGCAAGTTGTTGATCATCCACGTTATGGTAAACAATTAAAAGCAGAG
    ACTTTTGAAAAAGAAATGCCACAAACGAAAGAAGCAATTATAAGTTATTTATCTAGTGAT
    TTGTTTAAAGGTGTAGGTAAAAAGACAGCTCAAAATATTGTTAATACATTAGGTGACAAT
    GCGATAAATGATATATTAGATGACCATTCAGTGCTAGAAAAAGTTTCGGGATTATCTAAA
    AAGAAACAGAAACAAATTGCAGAACAAATTTCAGCAAATCAAGAATCTGAAAAAATAATG
    ATTCGTTTACATGATTTAGGGTTTGGTCCTAAACTTTCAATGGCAATTTATCAGTTTTAT
    CTCGGCGATACACTGACTATTTTAGATCGAAATCCATATCAATTGATTTATGATATTAAA
    GGTATTGGTTTTAATAAAGCAGATCAACTTGCTAGAAATATTGGTATCGCTTATAACGAT
    AATGAACGATTAAAAGCTGCGTTGCTCTATACGTTAGAAGAAGAATGTATTAAACAGGGA
    CATACATATTTGCCTATCAATGTTGTTATAGATTTAACGGTTGATGTATTAAATTATCAA
    GATGAAGAGGTCATCGAACCTGAAAAATTAGACGAAATGTTGCAATACTTAAATGAGGAA
    AAACGACTAATTATTGACAATGAACAAGTTGCAATTCCAAGTTTGTATTATTCTGAAATC
    AAAAGTGTTCAAAACTTATTCAGAATAAAGACGCATACAAATAAACTTACAGAAATTGAA
    CAGTCAGATTTACAAATGCATATTGGTGAAATAGAAGATGCGAATCAAGTGAACTATGCA
    GCTTCACAAAAAGAAGCTTTGCAAACGGCTATCAATTCTAAGGTGATGCTATTAACCGGT
    GGACCGGGAACAGGAAAAACGACAGTAATTAAAGGTATTGTTGAATTATATGCTGAGATT
    CATGGCTTATCATTAGATTATGATGATTATGTCAATGATGATTATCCAGTTGTATTAGCA
    GCGCCAACAGGAAGAGCGTCTAAGAGACTACAAGAGTCAACTGGATTAGAAGCAATGACG
    ATTCATCGTTTAATAGGTTGGAATCAAGACACAAAGCCAGAGGATATATTAGAAAATGAA
    ATAAACGCACGACTCATAATCATTGATGAGATGTCTATGGTAGATACTTGGTTGTTCCAC
    CAATTTTTAAGTGCAGTTCCTTTAGATGCACAATTGATATTTGTAGGTGATGAGGACCAA
    TTGCCTTCTGTAGGTCCTGGTCAAGTATTTAAAGATTTAATTGAATCGAAAGCTATACCA
    CGAGTAAATCTGACTGAAGTATATCGTCAACAAGATGGTTCAAGCATTATAGAATTAGCA
    CATCGAATGAAGTTGGGTCAGAAAATTGATATTACACAGCGTTTTCATGATAGAAGTTTT
    ATTAACTGTCAGGCAAACCAAATACCAACAGTTGTTGAGAAGGTAGTTACTAGTGCTGTT
    AATAAAGGGTATACTATGGCTGATATTCAAGTGCTTGCACCAATGTATAAAGGAAATGCC
    GGTATTAAACGTTTAAATCAAGTTTTACAAGATATTTTAAACCCTAAAAAGAAAGACACA
    CGAGAAATTGAGTTTGGTGATGTAGTCTTTAGAAAAGGTGACAAAGTATTACAACTTGTT
    AATAGGCCAAATGATAACATATTCAATGGTGACATAGGAGTTATTGTTGGTATTTTTTGG
    GCGAAAGAAAATGCCCTTAATAAAGATGTACTTGTTGTGGATTTTGAAGGTAATGAAATT
    ACATTTACGAAACAAGATATGATGGAATTAACACATGCTTATTGTACATCAATCCATAAA
    TCACAAGGTTCAGAATTTCCTATTGTTATCATGCCTATTGTTAAACAGTATTTTAGAATG
    TTACAAAGACCGATATTATATACTGGTTTAACTAGAGCGAAAACGAGTTTAGTTTTACTT
    GGTGATCCGGAAGCATTTGATATTGGATTGAAAACAAATGGTCAAGCGCGTTTAACACAA
    TTATGTACATTGTTGAAAAATTATTTTAATTCAGAAGATGAAGAAATGCTGGAAAACACA
    GCAACTAATGATACAGGAGCTTCACAAACGACAATAGATGATCAAGTAGAAGCGCCAATG
    TCATCGAATGATAGTGAAGAAGTTATGTCTGATTCAACAAAAACAGATACAAATGTATTA
    ACGGAAGCTACAATGTTTAAAATTGACCCAATGATTAATATGGGAGAAATCACGCCGTAT
    GACTTTATAGAACGTTGA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1260
    1320
    1380
    1440
    1500
    1560
    1620
    1680
    1740
    1800
    1860
    1920
    1980
    2040
    2100
    2160
    2220
    2280
    2340
    2400
    2460
    2478

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SACOL1674 [new locus tag: SACOL_RS08540 ]
  • symbol: SACOL1674
  • description: recombinase D
  • length: 825
  • theoretical pI: 4.48109
  • theoretical MW: 93048.2
  • GRAVY: -0.29103

⊟Function[edit | edit source]

  • reaction:
    EC 3.6.4.12?  ExPASy
    DNA helicase ATP + H2O = ADP + phosphate
  • TIGRFAM:
    Unknown function Enzymes of unknown specificity helicase, RecD/TraA family (TIGR01448; HMM-score: 1111.8)
    and 12 more
    Genetic information processing DNA metabolism DNA replication, recombination, and repair exodeoxyribonuclease V, alpha subunit (TIGR01447; EC 3.1.11.5; HMM-score: 229.4)
    Ti-type conjugative transfer relaxase TraA (TIGR02768; HMM-score: 101.5)
    conjugative transfer relaxase protein TraI (TIGR02760; EC 3.6.4.12; HMM-score: 29.4)
    Genetic information processing DNA metabolism DNA replication, recombination, and repair Holliday junction DNA helicase RuvA (TIGR00084; EC 3.6.4.12; HMM-score: 28.6)
    Cellular processes Cellular processes Sporulation and germination stage V sporulation protein K (TIGR02881; HMM-score: 25.2)
    Genetic information processing Protein fate Protein and peptide secretion and trafficking type VII secretion AAA-ATPase EccA (TIGR03922; HMM-score: 21.1)
    P-type DNA transfer ATPase VirB11 (TIGR02788; HMM-score: 16.2)
    Cellular processes Cellular processes Conjugation P-type conjugative transfer ATPase TrbB (TIGR02782; HMM-score: 12.6)
    CbbX protein (TIGR02880; HMM-score: 12.3)
    Genetic information processing Protein synthesis tRNA and rRNA base modification tRNA threonylcarbamoyl adenosine modification protein YjeE (TIGR00150; HMM-score: 12.1)
    helicase/secretion neighborhood ATPase (TIGR03819; HMM-score: 11.2)
    Genetic information processing Protein fate Protein and peptide secretion and trafficking signal recognition particle-docking protein FtsY (TIGR00064; HMM-score: 10.6)
  • TheSEED  :
    • RecD-like DNA helicase YrrC
    DNA Metabolism DNA repair DNA repair, bacterial RecBCD pathway  RecD-like DNA helicase YrrC
  • PFAM:
    P-loop_NTPase (CL0023) AAA_30; AAA domain (PF13604; HMM-score: 181.1)
    and 30 more
    AAA_19; AAA domain (PF13245; HMM-score: 128)
    HHH (CL0198) HHH_4; Helix-hairpin-helix containing domain (PF14490; HMM-score: 108.2)
    P-loop_NTPase (CL0023) UvrD_C_2; UvrD-like helicase C-terminal domain (PF13538; HMM-score: 58.3)
    AAA_11; AAA domain (PF13086; HMM-score: 33.9)
    Viral_helicase1; Viral (Superfamily 1) RNA helicase (PF01443; HMM-score: 29.5)
    HHH (CL0198) HHH_5; Helix-hairpin-helix domain (PF14520; HMM-score: 23.3)
    P-loop_NTPase (CL0023) AAA; ATPase family associated with various cellular activities (AAA) (PF00004; HMM-score: 20.2)
    AAA_18; AAA domain (PF13238; HMM-score: 19.7)
    T2SSE; Type II/IV secretion system protein (PF00437; HMM-score: 19.4)
    AAA_12; AAA domain (PF13087; HMM-score: 19.2)
    AAA_14; AAA domain (PF13173; HMM-score: 16.4)
    AAA_29; P-loop containing region of AAA domain (PF13555; HMM-score: 14.8)
    TsaE; Threonylcarbamoyl adenosine biosynthesis protein TsaE (PF02367; HMM-score: 14.7)
    NTPase_1; NTPase (PF03266; HMM-score: 14.7)
    ABC_tran; ABC transporter (PF00005; HMM-score: 14.5)
    Mg_chelatase; Magnesium chelatase, subunit ChlI (PF01078; HMM-score: 14.3)
    5_3_exonuc_C (CL0464) 5_3_exonuc; 5'-3' exonuclease, C-terminal SAM fold (PF01367; HMM-score: 14.3)
    HHH (CL0198) HHH_3; Helix-hairpin-helix motif (PF12836; HMM-score: 14.1)
    P-loop_NTPase (CL0023) Helicase_RecD; Helicase (PF05127; HMM-score: 13.9)
    AAA_28; AAA domain (PF13521; HMM-score: 13.8)
    AAA_22; AAA domain (PF13401; HMM-score: 13.7)
    AAA_16; AAA ATPase domain (PF13191; HMM-score: 13.6)
    RsgA_GTPase; RsgA GTPase (PF03193; HMM-score: 13.4)
    UvrD_C; UvrD-like helicase C-terminal domain (PF13361; HMM-score: 13.2)
    Zeta_toxin; Zeta toxin (PF06414; HMM-score: 12.7)
    NACHT; NACHT domain (PF05729; HMM-score: 12.5)
    DUF815; Protein of unknown function (DUF815) (PF05673; HMM-score: 12.1)
    PhoH; PhoH-like protein (PF02562; HMM-score: 11.4)
    AAA_5; AAA domain (dynein-related subfamily) (PF07728; HMM-score: 9.7)
    AAA_17; AAA domain (PF13207; HMM-score: 9.4)

⊟Structure, modifications & cofactors[edit | edit source]

  • domains:
  • modifications:
  • cofactors:
  • effectors:

⊟Localization[edit | edit source]

  • PSORTb: Cytoplasmic
    • Cytoplasmic Score: 7.5
    • Cytoplasmic Membrane Score: 1.15
    • Cellwall Score: 0.62
    • Extracellular Score: 0.73
    • Internal Helices: 0
  • LocateP: Intracellular
    • Prediction by SwissProt Classification: Cytoplasmic
    • Pathway Prediction: No pathway
    • Intracellular possibility: 1
    • Signal peptide possibility: -1
    • N-terminally Anchored Score: 1
    • Predicted Cleavage Site: No CleavageSite
  • SignalP: no predicted signal peptide
    • SP(Sec/SPI): 0.003329
    • TAT(Tat/SPI): 0.000112
    • LIPO(Sec/SPII): 0.000308
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MSDPTLFDYSMIKGTVEAILFQNSDNFYTVLKVDTIETNEDFDTMPTVVGFLPNIVEGDVYTFKGQVVDHPRYGKQLKAETFEKEMPQTKEAIISYLSSDLFKGVGKKTAQNIVNTLGDNAINDILDDHSVLEKVSGLSKKKQKQIAEQISANQESEKIMIRLHDLGFGPKLSMAIYQFYLGDTLTILDRNPYQLIYDIKGIGFNKADQLARNIGIAYNDNERLKAALLYTLEEECIKQGHTYLPINVVIDLTVDVLNYQDEEVIEPEKLDEMLQYLNEEKRLIIDNEQVAIPSLYYSEIKSVQNLFRIKTHTNKLTEIEQSDLQMHIGEIEDANQVNYAASQKEALQTAINSKVMLLTGGPGTGKTTVIKGIVELYAEIHGLSLDYDDYVNDDYPVVLAAPTGRASKRLQESTGLEAMTIHRLIGWNQDTKPEDILENEINARLIIIDEMSMVDTWLFHQFLSAVPLDAQLIFVGDEDQLPSVGPGQVFKDLIESKAIPRVNLTEVYRQQDGSSIIELAHRMKLGQKIDITQRFHDRSFINCQANQIPTVVEKVVTSAVNKGYTMADIQVLAPMYKGNAGIKRLNQVLQDILNPKKKDTREIEFGDVVFRKGDKVLQLVNRPNDNIFNGDIGVIVGIFWAKENALNKDVLVVDFEGNEITFTKQDMMELTHAYCTSIHKSQGSEFPIVIMPIVKQYFRMLQRPILYTGLTRAKTSLVLLGDPEAFDIGLKTNGQARLTQLCTLLKNYFNSEDEEMLENTATNDTGASQTTIDDQVEAPMSSNDSEEVMSDSTKTDTNVLTEATMFKIDPMINMGEITPYDFIER

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
  • protein localization: Cytoplasmic [1] [2] [3]
  • quantitative data / protein copy number per cell: 98 [4]
  • interaction partners:

⊟Expression & Regulation[edit | edit source]

⊟Operon[edit | edit source]

⊟Regulation[edit | edit source]

  • regulator:

⊟Transcription pattern[edit | edit source]

⊟Protein synthesis (provided by Aureolib)[edit | edit source]

⊟Protein stability[edit | edit source]

  • half-life: no data available

⊟Biological Material[edit | edit source]

⊟Mutants[edit | edit source]

⊟Expression vector[edit | edit source]

⊟lacZ fusion[edit | edit source]

⊟GFP fusion[edit | edit source]

⊟two-hybrid system[edit | edit source]

⊟FLAG-tag construct[edit | edit source]

⊟Antibody[edit | edit source]

⊟Other Information[edit | edit source]

You are kindly invited to share additional interesting facts.

⊟Literature[edit | edit source]

⊟References[edit | edit source]

  1. ↑ Dörte Becher, Kristina Hempel, Susanne Sievers, Daniela Zühlke, Jan Pané-Farré, Andreas Otto, Stephan Fuchs, Dirk Albrecht, Jörg Bernhardt, Susanne Engelmann, Uwe Völker, Jan Maarten van Dijl, Michael Hecker
    A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.
    PLoS One: 2009, 4(12);e8176
    [PubMed:19997597] [WorldCat.org] [DOI] (I e)
  2. ↑ Kristina Hempel, Florian-Alexander Herbst, Martin Moche, Michael Hecker, Dörte Becher
    Quantitative proteomic view on secreted, cell surface-associated, and cytoplasmic proteins of the methicillin-resistant human pathogen Staphylococcus aureus under iron-limited conditions.
    J Proteome Res: 2011, 10(4);1657-66
    [PubMed:21323324] [WorldCat.org] [DOI] (I p)
  3. ↑ Andreas Otto, Jan Maarten van Dijl, Michael Hecker, Dörte Becher
    The Staphylococcus aureus proteome.
    Int J Med Microbiol: 2014, 304(2);110-20
    [PubMed:24439828] [WorldCat.org] [DOI] (I p)
  4. ↑ Daniela Zühlke, Kirsten Dörries, Jörg Bernhardt, Sandra Maaß, Jan Muntel, Volkmar Liebscher, Jan Pané-Farré, Katharina Riedel, Michael Lalk, Uwe Völker, Susanne Engelmann, Dörte Becher, Stephan Fuchs, Michael Hecker
    Costs of life - Dynamics of the protein inventory of Staphylococcus aureus during anaerobiosis.
    Sci Rep: 2016, 6;28172
    [PubMed:27344979] [WorldCat.org] [DOI] (I e)

⊟Relevant publications[edit | edit source]

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